gapseq

https://gapseq.readthedocs.io/en/latest/
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### Run All Predictions

Source: https://gapseq.readthedocs.io/en/latest/_sources/usage/basics.md.txt

Execute all prediction steps with a single command. This is a quick way to get started.

```bash
./gapseq doall toy/myb71.faa.gz
```

--------------------------------

### Test Gapseq Installation on Ubuntu/Debian/Mint

Source: https://gapseq.readthedocs.io/en/latest/_sources/install.md.txt

Runs a test command to verify the Gapseq installation.

```sh
./gapseq test
```

--------------------------------

### Install Gapseq Dependencies on Ubuntu/Debian/Mint

Source: https://gapseq.readthedocs.io/en/latest/_sources/install.md.txt

Installs system dependencies, R packages, and downloads the Gapseq source code. Ensure you have git, build tools, and necessary libraries installed.

```sh
# Installation of main system dependencies
sudo apt install ncbi-blast+ git libglpk-dev r-base-core bc curl libcurl4-openssl-dev libssl-dev libsbml5-dev diamond-aligner mmseqs2

# installation of required R-packages
R -e 'install.packages(c("data.table", "stringr", "getopt", "R.utils", "stringi", "jsonlite", "httr", "pak"))'
R -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager"); BiocManager::install("Biostrings")'
R -e 'pak::pkg_install("Waschina/cobrar")'

# Download latest gapseq version from github
git clone https://github.com/jotech/gapseq && cd gapseq

# Download reference sequence database (Bacteria and Archaea)
bash ./gapseq update-sequences -t Bacteria
bash ./gapseq update-sequences -t Archaea
```

--------------------------------

### Install Gapseq System Dependencies with Homebrew

Source: https://gapseq.readthedocs.io/en/latest/_sources/install.md.txt

Installs core system dependencies for Gapseq using Homebrew on MacOS. Ensure Homebrew is installed and updated before running.

```bash
# Installation of main system dependencies
brew install coreutils binutils git glpk blast r grep bc gzip curl bc brewsci/bio/libsbml diamond mmseqs2
```

--------------------------------

### Install Specific Reference Sequence Database Version

Source: https://gapseq.readthedocs.io/en/latest/database/ReferenceSequences.html

Installs a specific version of the reference sequence database identified by a Zenodo record ID. This is crucial for ensuring reproducibility of results.

```bash
gapseq update-sequences -t Bacteria -Z <zenodoID>

```

--------------------------------

### Install Gapseq Dependencies on macOS with Homebrew

Source: https://gapseq.readthedocs.io/en/latest/install.html

Installs core system dependencies, R packages, and downloads the Gapseq source code from GitHub. This method is recommended for macOS users.

```bash
# Installation of main system dependencies
brew install coreutils binutils git glpk blast r grep bc gzip curl bc brewsci/bio/libsbml diamond mmseqs2

# installation of required R-packages
R -e 'install.packages(c("data.table", "stringr", "getopt", "R.utils", "stringi", "jsonlite", "httr"))'
R -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager"); BiocManager::install("Biostrings")'
R -e 'pak::pkg_install("Waschina/cobrar")'

# Download latest gapseq version from github
git clone https://github.com/jotech/gapseq && cd gapseq

# Download reference sequence database (Bacteria and Archaea)
bash ./gapseq update-sequences -t Bacteria
bash ./gapseq update-sequences -t Archaea
```

--------------------------------

### Install Gapseq Dependencies on Centos/Fedora/RHEL

Source: https://gapseq.readthedocs.io/en/latest/_sources/install.md.txt

Installs system dependencies, R packages, and downloads the Gapseq source code. Note that diamond and mmseqs2 are not installed via yum and require manual installation.

```sh
# Installation of main system dependencies
sudo yum install ncbi-blast+ git glpk-devel hmmer bc libcurl-devel curl openssl-devel libsbml-devel

# installation of required R-packages
R -e 'install.packages(c("data.table", "stringr", "getopt", "R.utils", "stringi", "jsonlite", "httr", "pak"))'
R -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager"); BiocManager::install("Biostrings")'
R -e 'pak::pkg_install("Waschina/cobrar")'

# Download latest gapseq version from github
git clone https://github.com/jotech/gapseq && cd gapseq

# Download reference sequence database (Bacteria and Archaea)
bash ./gapseq update-sequences -t Bacteria
bash ./gapseq update-sequences -t Archaea
```

--------------------------------

### Install a Specific Reference Sequence Database Version

Source: https://gapseq.readthedocs.io/en/latest/_sources/database/ReferenceSequences.md.txt

Installs a specific version of the reference sequence database identified by its Zenodo record ID. This is useful for ensuring reproducibility with older gapseq versions or specific datasets.

```sh
gapseq update-sequences -t Bacteria -Z <zenodoID>
```

--------------------------------

### Install libsbml Development Package

Source: https://gapseq.readthedocs.io/en/latest/_sources/install.md.txt

Installs the libsbml development package on Debian/Ubuntu or Fedora/CentOS systems. This is required for Gapseq's SBML support.

```sh
sudo apt install libsbml5-dev # debian/ubuntu
sudo yum install libsbml-devel # fedora/centos
```

--------------------------------

### Install 'cobrar' R Package from GitHub

Source: https://gapseq.readthedocs.io/en/latest/news.html

Install the 'cobrar' R package from GitHub using the 'remotes' package. Ensure system libraries 'libSBML' and 'glpk' are installed beforehand.

```r
remotes::install_github("Waschina/cobrar")
```

--------------------------------

### Biomass Component Example

Source: https://gapseq.readthedocs.io/en/latest/_sources/database/biomassReaction.md.txt

Example of a biomass component entry, specifying its ID, name, compartment, and coefficient.

```json
{
          "id"   : "cpd00161",
          "name" : "L-Threonine",
          "comp" : "c",
          "coef" : 0.0474316079511907,
          "link" : "cpd00001:-1"
        }
```

--------------------------------

### Basic Usage with Comma-Separated Lists

Source: https://gapseq.readthedocs.io/en/latest/_sources/usage/panDraft.md.txt

Provides a basic example of how to run the pan-draft module using comma-separated lists for model and pathway table paths.

```bash
gapseq pan -m MAG01-draft.RDS,MAG02-draft.RDS,MAG03-draft.RDS,MAG04-draft.RDS -w MAG01-all-Pathways.tbl,MAG02-all-Pathways.tbl,MAG03-all-Pathways.tbl,MAG04-all-Pathways.tbl
```

--------------------------------

### Example Reaction Table

Source: https://gapseq.readthedocs.io/en/latest/_sources/tutorials/archaea.md.txt

This table displays reaction IDs, names, fluxes, and equations for metabolic processes in methanogens, illustrating chemiosmosis.

```text
##            rxn                                                                           name     flux                                                                                                                           equation
##         <char>                                                                         <char>    <num>                                                                                                                             <char>
## 1: rxn90058_c0           Coenzyme B:coenzyme M:methanophenazine oxidoreductase (chemiosmosis) 16.59132 (3) H+-c0 + (1) CoM-S-S-CoB-c0 + (1) Dihydromethanophenazine-c0 <==> (1) CoM-c0 + (1) HTP-c0 + (1) Methanophenazine-c0 + (2) H+-e0
## 2: rxn90059_c0 hydrogen:2-(2,3-dihydropentaprenyloxy)phenazine oxidoreductase  (chemiosmosis) 16.59132                                     (2) H+-c0 + (1) Methanophenazine-c0 + (1) H2-c0 --> (1) Dihydromethanophenazine-c0 + (2) H+-e0
```

--------------------------------

### Install R 'remotes' Package

Source: https://gapseq.readthedocs.io/en/latest/news.html

Install the 'remotes' R package if it is not already installed. This is a prerequisite for installing packages from GitHub.

```r
install.packages("remotes") # only needed if 'remotes' is not installed yet
```

--------------------------------

### Install 'cobrar' R Package

Source: https://gapseq.readthedocs.io/en/latest/_sources/news.md.txt

Install the 'cobrar' R package, which replaces 'sybil' and 'sybilSBML' for metabolic modeling in Gapseq. Ensure 'remotes' is installed first if necessary.

```R
install.packages("remotes") # only needed if 'remotes' is not installed yet
```

```R
remotes::install_github("Waschina/cobrar")
```

--------------------------------

### Install Alternative Aligners (MMseqs2, Diamond)

Source: https://gapseq.readthedocs.io/en/latest/_sources/install.md.txt

Installs MMseqs2 and Diamond aligners on Debian/Ubuntu systems using apt. These tools can speed up Gapseq's find and find-transport modules.

```sh
sudo apt install mmseqs2 diamond-aligner
```

--------------------------------

### Install Stable Gapseq Release with Conda

Source: https://gapseq.readthedocs.io/en/latest/install.html

Creates and activates a conda environment for the stable Gapseq release and downloads the reference sequence databases. This is a convenient method for Linux and macOS.

```bash
conda create -c conda-forge -c bioconda -n gapseq gapseq

# activate gapseq environment
conda activate gapseq

# Download reference sequence database
gapseq update-sequences -t Bacteria
gapseq update-sequences -t Archaea
```

--------------------------------

### Integrate Pathway

Source: https://gapseq.readthedocs.io/en/latest/_sources/usage/adapt.md.txt

Integrate an entire pathway into a model, for example, the photosynthesis pathway into E. coli.

```bash
./gapseq adapt -a PHOTOALL-PWY -m toy/ecoli.RDS
```

--------------------------------

### Example Growth Medium Definition (CSV)

Source: https://gapseq.readthedocs.io/en/latest/usage/medium.html

Defines an M9-like medium with specific compound identifiers, names, and maximum flux rates. This format is used for gapfilling.

```csv
compounds,name,maxFlux
cpd00001,H2O,100
cpd00007,O2,10
cpd00009,Phosphate,100
cpd00027,D-Glucose,5
cpd00030,Mn2+,100
cpd00034,Zn2+,100
cpd00048,Sulfate,100
cpd00058,Cu2+,100
cpd00063,Ca2+,100
cpd00067,H+,100
cpd00099,Cl-,100
cpd00149,Co2+,100
cpd00205,K+,100
cpd00254,Mg,100
cpd00531,Hg2+,100
cpd00971,Na+,100
cpd01012,Cd2+,100
cpd01048,Arsenate,100
cpd10515,Fe2+,100
cpd10516,fe3,100
cpd11595,chromate,100
cpd00013,NH3,100

```

--------------------------------

### Download Sequence Database to a User Directory

Source: https://gapseq.readthedocs.io/en/latest/_sources/database/ReferenceSequences.md.txt

Downloads the reference sequence database to a specified user directory, useful when write permissions are limited in the default gapseq installation directory.

```sh
gapseq update-sequences -t Bacteria -D $HOME/gapseq_seqDB
```

--------------------------------

### Install Pyrodigal for Nucleotide Translation

Source: https://gapseq.readthedocs.io/en/latest/_sources/install.md.txt

Installs the Pyrodigal library using pip, which Gapseq uses for predicting open reading frames and translating nucleotide sequences to amino acids.

```sh
pip install pyrodigal
```

--------------------------------

### Install Development Version of Gapseq with Conda

Source: https://gapseq.readthedocs.io/en/latest/install.html

Clones the development version of Gapseq, creates a dedicated conda environment, and downloads the reference sequence databases. This method is for users who need the latest features.

```bash
# Cloning the development version of gapseq
git clone https://github.com/jotech/gapseq
cd gapseq

# Create and activate a conda environment "gapseq-dev"
conda env create -n gapseq-dev --file gapseq_env.yml
conda activate gapseq-dev

# Download reference sequence database (Bacteria and Archaea)
bash ./gapseq update-sequences -t Bacteria
bash ./gapseq update-sequences -t Archaea
```

--------------------------------

### Ensure R User Library is Writable

Source: https://gapseq.readthedocs.io/en/latest/_sources/install.md.txt

Run this command before installing R packages if you encounter 'is not writable' errors. It creates the user library directory if it doesn't exist.

```bash
Rscript -e 'if( file.access(Sys.getenv("R_LIBS_USER"), mode=2) == -1 ) dir.create(path = Sys.getenv("R_LIBS_USER"), showWarnings = FALSE, recursive = TRUE)'
```

--------------------------------

### Install Required R Packages for Gapseq

Source: https://gapseq.readthedocs.io/en/latest/_sources/install.md.txt

Installs necessary R packages for Gapseq functionality. This includes packages for data manipulation, string processing, and biological sequence analysis.

```r
R -e 'install.packages(c("data.table", "stringr", "getopt", "R.utils", "stringi", "jsonlite", "httr"))'
R -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager"); BiocManager::install("Biostrings")'
R -e 'pak::pkg_install("Waschina/cobrar")'
```

--------------------------------

### Create and Activate Conda Environment for Gapseq Development Version

Source: https://gapseq.readthedocs.io/en/latest/_sources/install.md.txt

Creates a Conda environment named 'gapseq-dev' using the 'gapseq_env.yml' file, which installs Gapseq and its dependencies. The environment is then activated.

```sh
# Create and activate a conda environment "gapseq-dev"
conda env create -n gapseq-dev --file gapseq_env.yml
conda activate gapseq-dev
```

--------------------------------

### Gapseq Command-Line Workflow for Archaea

Source: https://gapseq.readthedocs.io/en/latest/_sources/tutorials/archaea.md.txt

This sequence of commands outlines the gapseq workflow for finding genes, transporters, and drafting a metabolic model for archaea, starting with downloading a genome.

```sh
wget -q -O mthe.fna.gz ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/008/645/GCF_000008645.1_ASM864v1/GCF_000008645.1_ASM864v1_genomic.fna.gz

gapseq find -p all -t Archaea -m Archaea -A diamond mthe.fna.gz
gapseq find-transport -A diamond mthe.fna.gz
gapseq draft -r mthe-all-Reactions.tbl -t mthe-Transporter.tbl -u 200 -l 100 -p mthe-all-Pathways.tbl
gapseq fill -m mthe-draft.RDS -n ../../dat/media/MM_anaerobic_CO2_H2.csv -b 100 -e highH2
```

--------------------------------

### Clone Development Version of Gapseq

Source: https://gapseq.readthedocs.io/en/latest/_sources/install.md.txt

Clones the development version of Gapseq from GitHub and navigates into the gapseq directory. This is the first step for installing the latest development code.

```sh
# Cloning the development version of gapseq
git clone https://github.com/jotech/gapseq
cd gapseq
```

--------------------------------

### Ensure R Package Library is Writable

Source: https://gapseq.readthedocs.io/en/latest/install.html

Run this command before installing R packages if you encounter a 'not writable' error. It creates the user's library directory if it doesn't exist and ensures write permissions.

```bash
Rscript -e 'if( file.access(Sys.getenv("R_LIBS_USER"), mode=2) == -1 ) dir.create(path = Sys.getenv("R_LIBS_USER"), showWarnings = FALSE, recursive = TRUE)'

```

--------------------------------

### Find Sequences Using a User-Specified Database Directory

Source: https://gapseq.readthedocs.io/en/latest/_sources/database/ReferenceSequences.md.txt

Searches for sequences using a custom-specified reference sequence database location. This ensures gapseq uses the correct database when not using the default installation path.

```sh
gapseq find -p all -D $HOME/gapseq_seqDB -A diamond ecoli.faa.gz
```

--------------------------------

### Update Gapseq Sequence Databases

Source: https://gapseq.readthedocs.io/en/latest/_sources/install.md.txt

Downloads the reference sequence databases for Bacteria and Archaea using the gapseq update-sequences command. This command requires the gapseq tool to be cloned or installed.

```bash
# Download reference sequence database (Bacteria and Archaea)
bash ./gapseq update-sequences -t Bacteria
bash ./gapseq update-sequences -t Archaea
```

--------------------------------

### Example Growth Medium CSV/TSV Format

Source: https://gapseq.readthedocs.io/en/latest/_sources/usage/medium.md.txt

Defines a growth medium using a 3-column format: compounds identifier, compound name, and maximum flux. This format can be used for CSV or TSV files.

```text
compounds,name,maxFlux
cpd00001,H2O,100
cpd00007,O2,10
cpd00009,Phosphate,100
cpd00027,D-Glucose,5
cpd00030,Mn2+,100
cpd00034,Zn2+,100
cpd00048,Sulfate,100
cpd00058,Cu2+,100
cpd00063,Ca2+,100
cpd00067,H+,100
cpd00099,Cl-,100
cpd00149,Co2+,100
cpd00205,K+,100
cpd00254,Mg,100
cpd00531,Hg2+,100
cpd00971,Na+,100
cpd01012,Cd2+,100
cpd01048,Arsenate,100
cpd10515,Fe2+,100
cpd10516,fe3,100
cpd11595,chromate,100
cpd00013,NH3,100
```

--------------------------------

### Recommended Usage with Directory Paths

Source: https://gapseq.readthedocs.io/en/latest/_sources/usage/panDraft.md.txt

Illustrates the recommended method for pan-draft input by specifying directories containing the draft model and pathway prediction files.

```bash
mkdir -p modfiles
mv MAG*-draft.RDS modfiles
mv MAG*-all-Pathways.tbl modfiles
gapseq pan -m modfiles/ -w modfiles/
```

--------------------------------

### Create Draft Model

Source: https://gapseq.readthedocs.io/en/latest/usage/basics.html

Creates a draft model using reaction, transporter, and pathway table files as input.

```bash
./gapseq draft -r toy/myb71-all-Reactions.tbl -t toy/myb71-Transporter.tbl -p toy/myb71-all-Pathways.tbl

```

--------------------------------

### Basic Usage with Wildcards

Source: https://gapseq.readthedocs.io/en/latest/_sources/usage/panDraft.md.txt

Demonstrates using wildcards to specify paths for draft models and pathway prediction tables.

```bash
gapseq pan -m MAG*-draft.RDS -w MAG*-all-Pathways.tbl
```

--------------------------------

### Biomass Group Definition Example

Source: https://gapseq.readthedocs.io/en/latest/_sources/database/biomassReaction.md.txt

Example of a biomass group definition, including group name, mass, unit type, and a list of components.

```json
{
      "group_name" : "Lipids",
      "mass" : 0.09,
      "unit_group" : "g",
      "unit_components" : "MOLSPLIT",
      "components" : [
        {
          "id"   : "cpd15540",
          "name" : "Phosphatidylglycerol-dioctadecanoyl",
          "comp" : "c",
          "coef" : 1
        },
        {
          "id"   : "cpd15793",
          "name" : "Stearoylcardiolipin-B-subtilis",
          "comp" : "c",
          "coef" : 1
        },
        {
          "id"   : "cpd15722",
          "name" : "Diisoheptadecanoylphosphatidylglycerol",
          "comp" : "c",
          "coef" : 1
        },
        {
          "id"   : "cpd15794",
          "name" : "Isoheptadecanoylcardiolipin-B-subtilis",
          "comp" : "c",
          "coef" : 1
        },
        {
          "id"   : "cpd15723",
          "name" : "Dianteisoheptadecanoylphosphatidylglycerol",
          "comp" : "c",
          "coef" : 1
        },
        {
          "id"   : "cpd15795",
          "name" : "Anteisoheptadecanoylcardiolipin-B-subtilis",
          "comp" : "c",
          "coef" : 1
        },
        {
          "id"   : "cpd15533",
          "name" : "phosphatidylethanolamine-dioctadecanoyl",
          "comp" : "c",
          "coef" : 1
        },
        {
          "id"   : "cpd15696",
          "name" : "Dianteisoheptadecanoylphosphatidylethanolamine",
          "comp" : "c",
          "coef" : 1
        },
        {
          "id"   : "cpd15695",
          "name" : "Diisoheptadecanoylphosphatidylethanolamine",
          "comp" : "c",
          "coef" : 1
        }
      ]
    }
```

--------------------------------

### Enable Substance Uptake

Source: https://gapseq.readthedocs.io/en/latest/_sources/usage/adapt.md.txt

Enable the uptake of a specific substance for a model to allow growth under a known condition. Requires a table of all reactions.

```bash
./gapseq adapt -m toy/myb71.RDS -w cpd00211:TRUE -b toy/myb71-all-Reactions.tbl
```

--------------------------------

### Create Draft Metabolic Model

Source: https://gapseq.readthedocs.io/en/latest/_sources/usage/basics.md.txt

Generate a draft metabolic model using provided reaction, transporter, and pathway tables. This is the initial step in network reconstruction.

```bash
./gapseq draft -r toy/myb71-all-Reactions.tbl -t toy/myb71-Transporter.tbl -p toy/myb71-all-Pathways.tbl
```

--------------------------------

### Download Genome Assemblies and Media File

Source: https://gapseq.readthedocs.io/en/latest/tutorials/yogurt.html

Downloads the protein sequences for Lactobacillus delbrueckii and Streptococcus thermophilus from NCBI RefSeq, and the milk growth media file from a GitHub repository. These commands are used to prepare the input data for gapseq.

```bash
# Download genome assemblies from NCBI (RefSeq) in protein sequences
wget -q -O ldel.faa.gz ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/056/065/GCF_000056065.1_ASM5606v1/GCF_000056065.1_ASM5606v1_protein.faa.gz
wget -q -O sthe.faa.gz ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/010/120/595/GCF_010120595.1_ASM1012059v1/GCF_010120595.1_ASM1012059v1_protein.faa.gz

# Download gapfill-medium file from github
wget -q https://github.com/Waschina/gapseq.tutorial.data/raw/master/yogurt/milk.csv

```

--------------------------------

### Remove Pathway

Source: https://gapseq.readthedocs.io/en/latest/_sources/usage/adapt.md.txt

Remove an entire pathway from a model, for example, the glycolysis pathway.

```bash
./gapseq adapt -m toy/ecoli.RDS -r GLYCOLYSIS
```

--------------------------------

### Load data.table Package

Source: https://gapseq.readthedocs.io/en/latest/_sources/tutorials/yogurt.md.txt

Loads the data.table package for efficient data manipulation and summarization of FBA/FVA results. Ensure this package is installed before running.

```r
library(data.table)
```

--------------------------------

### Predict Gapfill Medium for Pan-Model

Source: https://gapseq.readthedocs.io/en/latest/_sources/tutorials/pandraft.md.txt

Predicts a minimal growth medium that supports biomass production for the pan-model. This step is crucial for making the draft model functional.

```sh
# predict gapfill medium for pan model
gapseq medium -m pan_model/panModel-draft.RDS -p pan_model/panModel-tmp-Pathways.tbl -f pan_model/
```

--------------------------------

### Use MMseqs2 Aligner with Gapseq

Source: https://gapseq.readthedocs.io/en/latest/_sources/install.md.txt

Specifies the MMseqs2 aligner for the 'gapseq find' and 'gapseq find-transport' modules. Ensure MMseqs2 is installed and in your system's PATH.

```sh
# mmseqs2
gapseq find -p all -A mmseqs2 genome.faa.gz
gapseq find-transport -p all -A mmseqs2 genome.faa.gz
```

--------------------------------

### Download Genome Assemblies and Media File

Source: https://gapseq.readthedocs.io/en/latest/_sources/tutorials/yogurt.md.txt

Download the necessary protein FASTA files for Lactobacillus delbrueckii and Streptococcus thermophilus, along with the milk growth media CSV file from GitHub.

```sh
# Download genome assemblies from NCBI (RefSeq) in protein sequences
wget -q -O ldel.faa.gz ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/056/065/GCF_000056065.1_ASM5606v1/GCF_000056065.1_ASM5606v1_protein.faa.gz
wget -q -O sthe.faa.gz ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/010/120/595/GCF_010120595.1_ASM1012059v1/GCF_010120595.1_ASM1012059v1_protein.faa.gz

# Download gapfill-medium file from github
wget -q https://github.com/Waschina/gapseq.tutorial.data/raw/master/yogurt/milk.csv
```

--------------------------------

### Use Diamond Aligner with Gapseq

Source: https://gapseq.readthedocs.io/en/latest/_sources/install.md.txt

Specifies the Diamond aligner for the 'gapseq find' and 'gapseq find-transport' modules. Ensure Diamond is installed and in your system's PATH.

```sh
# diamond
gapseq find -p all -A diamond genome.faa.gz
gapseq find-transport -p all -A diamond genome.faa.gz
```

--------------------------------

### Find Metabolic Pathways

Source: https://gapseq.readthedocs.io/en/latest/usage/basics.html

Searches for all metabolic pathways. Requires a FASTA file as input.

```bash
./gapseq find -p all toy/myb71.faa.gz

```

--------------------------------

### Update Reference Sequences for Archaea

Source: https://gapseq.readthedocs.io/en/latest/_sources/database/ReferenceSequences.md.txt

Installs or updates the reference sequence database for archaea. This command fetches the latest sequences associated with the current gapseq version.

```sh
gapseq update-sequences -t Archaea # for archaea
```

--------------------------------

### Update Reference Sequences for Bacteria

Source: https://gapseq.readthedocs.io/en/latest/_sources/database/ReferenceSequences.md.txt

Installs or updates the reference sequence database for bacteria. This command fetches the latest sequences associated with the current gapseq version.

```sh
gapseq update-sequences -t Bacteria # for bacteria
```

--------------------------------

### Load cobrapy and data.table R Packages

Source: https://gapseq.readthedocs.io/en/latest/tutorials/yogurt.html

Loads the necessary R packages, cobrapy for metabolic modeling and data.table for data manipulation. Ensure these packages are installed before running.

```r
library(cobrar)

```

```r
library(data.table)

```

--------------------------------

### Update Reference Sequences for Bacteria or Archaea

Source: https://gapseq.readthedocs.io/en/latest/database/ReferenceSequences.html

Installs or updates the reference sequence databases for gapseq. Specify the target domain ('Bacteria' or 'Archaea') to download the appropriate sequences.

```bash
gapseq update-sequences -t Bacteria # for bacteria
gapseq update-sequences -t Archaea # for archaea

```

--------------------------------

### Build Pan-Draft Model

Source: https://gapseq.readthedocs.io/en/latest/_sources/tutorials/pandraft.md.txt

Combines individual draft metabolic models into a single pan-draft model, capturing shared and accessory metabolic reactions.

```sh
# reconstruct pan model
mkdir -p pan_model
gapseq pan -m models/ -w models/ -f pan_model/
```

--------------------------------

### Predict Growth Medium Command

Source: https://gapseq.readthedocs.io/en/latest/_sources/usage/medium.md.txt

Predicts a growth medium using pathway and draft model inputs. Use this to generate a gapfilling medium.

```bash
gapseq medium -m ecoli-draft.RDS -p ecoli-all-Pathways.tbl
```

--------------------------------

### Fill Metabolic Model with Gapseq

Source: https://gapseq.readthedocs.io/en/latest/_sources/tutorials/archaea.md.txt

Fills the draft metabolic model using specified media and biomass constraints with gapseq.

```sh
gapseq fill -m mbar-draft.RDS -n ../../dat/media/MM_anaerobic_CO2_H2.csv -b 100 -e highH2
```

--------------------------------

### Download Genome and Run gapseq for Methanogens

Source: https://gapseq.readthedocs.io/en/latest/tutorials/archaea.html

Downloads the genome of Methanothermobacter thermautotrophicus and runs gapseq to find metabolic pathways and transporters. This is for methanogens without cytochromes.

```bash
wget -q -O mthe.fna.gz ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/008/645/GCF_000008645.1_ASM864v1/GCF_000008645.1_ASM864v1_genomic.fna.gz

gapseq find -p all -t Archaea -m Archaea -A diamond mthe.fna.gz
gapseq find-transport -A diamond mthe.fna.gz
gapseq draft -r mthe-all-Reactions.tbl -t mthe-Transporter.tbl -u 200 -l 100 -p mthe-all-Pathways.tbl
gapseq fill -m mthe-draft.RDS -n ../../dat/media/MM_anaerobic_CO2_H2.csv -b 100 -e highH2

```

--------------------------------

### Download and Clone Gapseq from GitHub

Source: https://gapseq.readthedocs.io/en/latest/_sources/install.md.txt

Clones the latest Gapseq version from GitHub and navigates into the gapseq directory. This is a prerequisite for updating sequence databases.

```bash
# Download latest gapseq version from github
git clone https://github.com/jotech/gapseq && cd gapseq
```

--------------------------------

### Update to the Latest Reference Sequence Database

Source: https://gapseq.readthedocs.io/en/latest/_sources/database/ReferenceSequences.md.txt

Updates the reference sequence database to the absolute latest version available on Zenodo, overriding the version-specific database linked to the current gapseq installation.

```sh
gapseq update-sequences -t Bacteria -Z latest
```

--------------------------------

### Draft Metabolic Model with Gapseq

Source: https://gapseq.readthedocs.io/en/latest/_sources/tutorials/archaea.md.txt

Creates a draft metabolic model by combining identified reactions, transporters, and pathways using gapseq.

```sh
gapseq draft -r mbar-all-Reactions.tbl -t mbar-Transporter.tbl -u 200 -l 100 -p mbar-all-Pathways.tbl
```

--------------------------------

### Combine Growth Phenotype Modifications

Source: https://gapseq.readthedocs.io/en/latest/_sources/usage/adapt.md.txt

Combine enabling and disabling of growth phenotypes in a single command by providing a list of substances with their desired growth state. Requires a table of all reactions.

```bash
./gapseq adapt -m toy/myb71.RDS -w cpd00211:TRUE,cpd00027:FALSE -b toy/myb71-all-Reactions.tbl
```

--------------------------------

### Fill metabolic model with media

Source: https://gapseq.readthedocs.io/en/latest/tutorials/archaea.html

Fills the metabolic model using a specified media composition and high hydrogen conditions. This step refines the model for constraint-based analysis.

```bash
gapseq fill -m mbar-draft.RDS -n ../../dat/media/MM_anaerobic_CO2_H2.csv -b 100 -e highH2

```

--------------------------------

### Find Specific Pathways

Source: https://gapseq.readthedocs.io/en/latest/usage/basics.html

Searches for a specific metabolic pathway, like 'chitin'. Requires a FASTA file.

```bash
./gapseq find -p chitin toy/myb71.faa.gz

```

--------------------------------

### Example user-defined biomass JSON format

Source: https://gapseq.readthedocs.io/en/latest/_sources/database/biomassReaction.md.txt

This JSON structure defines a custom biomass reaction. It includes metadata like ID, name, and domain, along with detailed component groups (e.g., DNA, RNA, Protein) and their constituent metabolites with coefficients.

```json
{
  "id" : "user_biomass",
  "name" : "A user biomass definition",
  "ref"  : "Motivated by https://github.com/jotech/gapseq/issues/156",
  "energy_GAM" :  40,
  "domain" : "Bacteria",
  "met_groups" : [
    {
      "group_name" : "DNA",
      "mass" : 0.03,
      "unit_group" : "g",
      "unit_components" : "MOLFRACTION",
      "components" : [
        
        {
          "id"   : "cpd00115",
          "name" : "dATP",
          "comp" : "c",
          "coef" : 0.25,
          "link" : "cpd00012:-1"
        },
        
        {
          "id"   : "cpd00357",
          "name" : "dTTP",
          "comp" : "c",
          "coef" : 0.25,
          "link" : "cpd00012:-1"
        },
        
        {
          "id"   : "cpd00241",
          "name" : "dGTP",
          "comp" : "c",
          "coef" : 0.25,
          "link" : "cpd00012:-1"
        },
        
        {
          "id"   : "cpd00356",
          "name" : "dCTP",
          "comp" : "c",
          "coef" : 0.25,
          "link" : "cpd00012:-1"
        }
        
      ]
    },
    
    {
      "group_name" : "RNA",
      "mass" : 0.2,
      "unit_group" : "g",
      "unit_components" : "MOLFRACTION",
      "components" : [
        
        {
          "id"   : "cpd00002",
          "name" : "ATP",
          "comp" : "c",
          "coef" : 0.25,
          "link" : "cpd00012:-1"
        },
        
        {
          "id"   : "cpd00062",
          "name" : "UTP",
          "comp" : "c",
          "coef" : 0.25,
          "link" : "cpd00012:-1"
        },
        
        {
          "id"   : "cpd00038",
          "name" : "GTP",
          "comp" : "c",
          "coef" : 0.25,
          "link" : "cpd00012:-1"
        },
        
        {
          "id"   : "cpd00052",
          "name" : "CTP",
          "comp" : "c",
          "coef" : 0.25,
          "link" : "cpd00012:-1"
        }
        
      ]
    },
    
    {
      "group_name" : "Protein",
      "mass" : 0.55,
      "unit_group" : "g",
      "unit_components" : "MOLFRACTION",
      "components" : [
        
        {
          "id"   : "cpd00035",
          "name" : "L-alanine",
          "comp" : "c",
          "coef" : 0.1,
          "link" : "cpd00001:-1"
        },
        
        {
          "id"   : "cpd00051",
          "name" : "L-arginine",
          "comp" : "c",
          "coef" : 0.05,
          "link" : "cpd00001:-1"
        },
        
        {
          "id"   : "cpd00132",
          "name" : "L-asparagine",
          "comp" : "c",
          "coef" : 0.05,
          "link" : "cpd00001:-1"
        },
        
        {
          "id"   : "cpd00041",
          "name" : "L-Aspartate",
          "comp" : "c",
          "coef" : 0.05,
          "link" : "cpd00001:-1"
        },
        
        {
          "id"   : "cpd00084",
          "name" : "L-Cysteine",
          "comp" : "c",
          "coef" : 0.01,
          "link" : "cpd00001:-1"
        },
        
        {
          "id"   : "cpd00053",
          "name" : "L-Glutamine",
          "comp" : "c",
          "coef" : 0.05,
          "link" : "cpd00001:-1"
        },
        
        {
          "id"   : "cpd00023",
          "name" : "L-Glutamate",
          "comp" : "c",
          "coef" : 0.06,
          "link" : "cpd00001:-1"
        },
        
        {
          "id"   : "cpd00033",
          "name" : "Glycine",
          "comp" : "c",
          "coef" : 0.1,
          "link" : "cpd00001:-1"
        },
        
        {
          "id"   : "cpd00119",
          "name" : "L-Histidine",
          "comp" : "c",
          "coef" : 0.02,
          "link" : "cpd00001:-1"
        },
        
        {
          "id"   : "cpd00322",
          "name" : "L-Isoleucine",
          "comp" : "c",
          "coef" : 0.05,
          "link" : "cpd00001:-1"
        },
        
        {
          "id"   : "cpd00107",
          "name" : "L-Leucine",
          "comp" : "c",
          "coef" : 0.09,
          "link" : "cpd00001:-1"
        },
        
        {
          "id"   : "cpd00039",
          "name" : "L-Lysine",
          "comp" : "c",
          "coef" : 0.05,
          "link" : "cpd00001:-1"
        }
      ]
    }
  ]
}
```

--------------------------------

### Predict Growth Medium

Source: https://gapseq.readthedocs.io/en/latest/usage/medium.html

Predicts a growth medium using pathway prediction and draft model inputs. Requires specifying the draft model and pathway table.

```bash
gapseq medium -m ecoli-draft.RDS -p ecoli-all-Pathways.tbl

```
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